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Structure paper

TitleMolecular basis of immune evasion by the Delta and Kappa SARS-CoV-2 variants.
Journal, issue, pagesScience, Vol. 374, Issue 6575, Page 1621-1626, Year 2021
Publish dateDec 24, 2021
AuthorsMatthew McCallum / Alexandra C Walls / Kaitlin R Sprouse / John E Bowen / Laura E Rosen / Ha V Dang / Anna De Marco / Nicholas Franko / Sasha W Tilles / Jennifer Logue / Marcos C Miranda / Margaret Ahlrichs / Lauren Carter / Gyorgy Snell / Matteo Samuele Pizzuto / Helen Y Chu / Wesley C Van Voorhis / Davide Corti / David Veesler /
PubMed AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission leads to the emergence of variants, including the B.1.617.2 (Delta) variant of concern that is causing a new wave of ...Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission leads to the emergence of variants, including the B.1.617.2 (Delta) variant of concern that is causing a new wave of infections and has become globally dominant. We show that these variants dampen the in vitro potency of vaccine-elicited serum neutralizing antibodies and provide a structural framework for describing their immune evasion. Mutations in the B.1.617.1 (Kappa) and Delta spike glycoproteins abrogate recognition by several monoclonal antibodies via alteration of key antigenic sites, including remodeling of the Delta amino-terminal domain. The angiotensin-converting enzyme 2 binding affinities of the Kappa and Delta receptor binding domains are comparable to the Wuhan-Hu-1 isolate, whereas B.1.617.2+ (Delta+) exhibits markedly reduced affinity.
External linksScience / PubMed:34751595
MethodsEM (single particle)
Resolution2.4 - 3.6 Å
Structure data

25263

7so9

EMDB-25263, PDB-7so9:
SARS-CoV-2 S B.1.617.2 delta variant + S2M11 + S2L20 Global Refinement
Method: EM (single particle) / Resolution: 2.4 Å

25264

7soa

EMDB-25264, PDB-7soa:
SARS-CoV-2 S NTD B.1.617.2 delta variant + S2L20 Local Refinement
Method: EM (single particle) / Resolution: 3.1 Å

25265

7sob

EMDB-25265, PDB-7sob:
SARS-CoV-2 S B.1.617.1 kappa variant + S309 + S2L20 Global Refinement
Method: EM (single particle) / Resolution: 2.4 Å

25266

7soc

EMDB-25266, PDB-7soc:
SARS-CoV-2 S RBD B.1.617.1 kappa variant S309 Local Refinement
Method: EM (single particle) / Resolution: 3.3 Å

25267

7sod

EMDB-25267, PDB-7sod:
SARS-CoV-2 S NTD B.1.617.1 kappa variant S2L20 Local Refinement
Method: EM (single particle) / Resolution: 3.2 Å

25268

7soe

EMDB-25268, PDB-7soe:
SARS-CoV-2 S B.1.617.1 kappa variant + S2X303 Global Refinement
Method: EM (single particle) / Resolution: 2.8 Å

25269

7sof

EMDB-25269, PDB-7sof:
SARS-CoV-2 S NTD B.1.617.1 kappa variant S2X303 Local Refinement
Method: EM (single particle) / Resolution: 3.6 Å

Chemicals

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine

ChemComp-HOH:
WATER / Water

Source
  • severe acute respiratory syndrome coronavirus 2
  • homo sapiens (human)
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / delta / spike / antibody / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / VIRAL PROTEIN-IMMUNE SYSTEM complex / kappa

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